As glycoscience advances, labs will increasingly want to ask questions about glycosylation sites on a protein or the structure of a sugar, says Raja Mazumder, a bioinformatician at George Washington University. They might ask for example: are there glycosyltransferases that are expressed in liver but not in the heart, or, which ones are overexpressed by a factor of three in more than two cancers. Such questions require infrastructure building, he says, because right now there is no mechanism to allow such queries. But he and others are building such capabilities. Mazumder along with William York at the University of Georgia are starting to build a glycoscience informatics portal. Read more
As discussed in this month’s Editorial, the Protein Structure Initiative (PSI), a 15-year, nearly $1 billion structural genomics project funded by the National Institute of General Medical Sciences (NIGMS), will be coming to an end in 2015. The impact of ending this project should be minimized to avoid the loss of valuable resources and expertise. Read more
People, publishing, and policy: Q&A with Janet Thornton, director of the European Bioinformatics Institute.
The scientist profiled in the February issue of Nature Methods (the Author File) is Janet Thornton, the director of the European Bioinformatics Institute. Read more
Neil Kelleher and Lloyd Smith propose that the scientific community adopt the term ‘proteoform’ to refer to all the different forms that a protein can take. Will the community adopt it? Read more
Our choice of Method of the Year in prior years has tended to be methods that generally didn’t even exist only a few years earlier but which had quickly bounded onto the scientific stage and attracted the attention of a large portion of the scientific community. Targeted proteomics, our choice for 2012, on the other hand has existed for years in scaled-down forms using methods based on antibodies. Western blotting, immunofluorescence, antibody arrays, etc. can all be used to detect and measure targeted subsets the proteins expressed in cells and tissues. Read more
Many in the mass spectrometry community agree that MS data should be made publicly available for everybody’s benefit. All data, including the raw files generated by the mass spectrometers. Read more
The Louis-Jeantet Foundation awarded its prestigious 2012 Louis-Jeantet Prize for medicine to Matthias Mann last Tuesday, Jan 24th, for his contributions to mass spectrometry and the field of proteomics. Matthias Mann, Director of the Department of Proteomics and Signal Transduction at the Max-Planck Institute of Biochemistry in Martinsried, and his co-workers have developed several of the key technologies that have made modern proteomics possible, including mass spectrometry-based identification of proteins from electrophoretic gels and the SILAC method that underlies many recent quantitative proteomics studies. The foundation highlighted, in particular, his quantitative analyses of cancer cell proteomes, and the promise this work may hold for the future diagnosis and treatment of cancer (e.g. Geiger et al, 2010; Lundberg et al, 2010; Nagaraj et al, 2011). Read more